<classpathentry kind="lib" path="testsrc/lib/testng-5.10-jdk15.jar"/>\r
<classpathentry kind="lib" path="lib/servlet-api.jar"/>\r
<classpathentry kind="lib" path="WEB-INF/lib/drmaa.jar"/>\r
- <classpathentry kind="lib" path="WEB-INF/lib/compbio-annotations-1.0.jar"/>\r
<classpathentry kind="lib" path="WEB-INF/lib/compbio-util-1.3.jar"/>\r
- <classpathentry kind="lib" path="binaries/aaconservation.jar"/>\r
+ <classpathentry kind="lib" path="WEB-INF/lib/compbio-annotations-1.0.jar"/>\r
<classpathentry kind="output" path="WEB-INF/classes"/>\r
</classpath>\r
--- /dev/null
+/*
+ * Copyright (c) 2010 Agnieszka Golicz & Peter Troshin
+ *
+ * Amino Acid Conservation @version: 1.0
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the Apache License version 2 as published by the
+ * Apache Software Foundation This library is distributed in the hope that it
+ * will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
+ * License for more details. A copy of the license is in apache_license.txt. It
+ * is also available here: http://www.apache.org/licenses/LICENSE-2.0.txt
+ * Any republication or derived work distributed in source code form must
+ * include this copyright and license notice.
+ *
+ */
+package compbio.data.sequence;
+
+/**
+ * Enumeration listing of all the supported methods.
+ *
+ * @author Agnieszka Golicz & Peter Troshin
+ */
+public enum Method {
+ KABAT, JORES, SCHNEIDER, SHENKIN, GERSTEIN, TAYLOR_GAPS, TAYLOR_NO_GAPS, ZVELIBIL, KARLIN, ARMON, THOMPSON, NOT_LANCET, MIRNY, WILLIAMSON, LANDGRAF, SANDER, VALDAR, SMERFS;
+
+ public static Method getMethod(String meth) {
+ meth = meth.trim().toLowerCase();
+ if (meth.equalsIgnoreCase(KABAT.toString())) {
+ return KABAT;
+ }
+ if (meth.equalsIgnoreCase(JORES.toString())) {
+ return JORES;
+ }
+ if (meth.equalsIgnoreCase(SCHNEIDER.toString())) {
+ return SCHNEIDER;
+ }
+ if (meth.equalsIgnoreCase(SHENKIN.toString())) {
+ return SHENKIN;
+ }
+ if (meth.equalsIgnoreCase(GERSTEIN.toString())) {
+ return GERSTEIN;
+ }
+ if (meth.equalsIgnoreCase(TAYLOR_GAPS.toString())) {
+ return TAYLOR_GAPS;
+ }
+ if (meth.equalsIgnoreCase(TAYLOR_NO_GAPS.toString())) {
+ return TAYLOR_NO_GAPS;
+ }
+ if (meth.equalsIgnoreCase(ZVELIBIL.toString())) {
+ return ZVELIBIL;
+ }
+ if (meth.equalsIgnoreCase(KARLIN.toString())) {
+ return KARLIN;
+ }
+ if (meth.equalsIgnoreCase(ARMON.toString())) {
+ return ARMON;
+ }
+ if (meth.equalsIgnoreCase(THOMPSON.toString())) {
+ return THOMPSON;
+ }
+ if (meth.equalsIgnoreCase(NOT_LANCET.toString())) {
+ return NOT_LANCET;
+ }
+ if (meth.equalsIgnoreCase(MIRNY.toString())) {
+ return MIRNY;
+ }
+ if (meth.equalsIgnoreCase(WILLIAMSON.toString())) {
+ return WILLIAMSON;
+ }
+ if (meth.equalsIgnoreCase(LANDGRAF.toString())) {
+ return LANDGRAF;
+ }
+ if (meth.equalsIgnoreCase(SANDER.toString())) {
+ return SANDER;
+ }
+ if (meth.equalsIgnoreCase(VALDAR.toString())) {
+ return VALDAR;
+ }
+ if (meth.equalsIgnoreCase(SMERFS.toString())) {
+ return SMERFS;
+ }
+ return null;
+ }
+
+}
import javax.xml.bind.annotation.XmlAccessType;\r
import javax.xml.bind.annotation.XmlAccessorType;\r
\r
-import compbio.conservation.Method;\r
import compbio.util.annotation.Immutable;\r
\r
@XmlAccessorType(XmlAccessType.FIELD)\r
import java.util.regex.Matcher;\r
import java.util.regex.Pattern;\r
\r
-import compbio.conservation.Method;\r
-\r
/**\r
* Utility class for operations on sequences\r
* \r
*/\r
private int ncoreNumber = 0;\r
\r
- private final String ncorePrm = "-n=";\r
+ private final String ncorePrm = "-t=";\r
\r
// Cache for Limits information\r
private static LimitsManager<AACon> limits;\r
\r
- public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+ public static final String KEY_VALUE_SEPARATOR = "=";\r
public static final String STAT_FILE = "stat.txt";\r
\r
public AACon() {\r
import org.testng.annotations.BeforeMethod;\r
import org.testng.annotations.Test;\r
\r
-import compbio.conservation.Method;\r
+import compbio.data.sequence.Method;\r
import compbio.data.sequence.MultiAnnotatedSequence;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import java.io.FileInputStream;\r
import java.io.FileNotFoundException;\r
import java.io.IOException;\r
+import java.net.MalformedURLException;\r
import java.net.URL;\r
+import java.util.ArrayList;\r
import java.util.HashSet;\r
import java.util.List;\r
\r
import javax.xml.namespace.QName;\r
import javax.xml.ws.Service;\r
\r
+import org.testng.annotations.BeforeTest;\r
import org.testng.annotations.Test;\r
\r
-import compbio.conservation.Method;\r
import compbio.data.msa.Annotation;\r
import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Method;\r
import compbio.data.sequence.Score;\r
import compbio.data.sequence.SequenceUtil;\r
import compbio.metadata.JobSubmissionException;\r
import compbio.metadata.LimitExceededException;\r
+import compbio.metadata.PresetManager;\r
import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.RunnerConfig;\r
import compbio.metadata.UnsupportedRuntimeException;\r
+import compbio.metadata.WrongParameterException;\r
+import compbio.runner.conservation.AACon;\r
import compbio.util.SysPrefs;\r
-import compbio.ws.server.AAConWS;\r
\r
public class TestAAConWS {\r
\r
- @Test\r
- public void test() throws FileNotFoundException, IOException {\r
+ Annotation<AACon> msaws;\r
\r
- URL url = new URL("http://localhost:8080/jabaws/AAConWS?wsdl");\r
+ @BeforeTest\r
+ void initConnection() {\r
+ URL url = null;\r
+ try {\r
+ url = new URL("http://localhost:8080/jabaws/AAConWS?wsdl");\r
+ } catch (MalformedURLException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
String namespace = "http://msa.data.compbio/01/12/2010/";\r
QName qname = new QName(namespace, "AAConWS");\r
Service serv = Service.create(url, qname);\r
+ msaws = serv.getPort(new QName(namespace, "AAConWSPort"),\r
+ Annotation.class);\r
+ }\r
+\r
+ @Test\r
+ public void testAnalize() throws FileNotFoundException, IOException {\r
+\r
/*\r
* MsaWS msaws = serv.getPort(new QName(\r
* "http://msa.data.compbio/01/01/2010/", "ClustalWSPort"),\r
// Annotation<AACon> msaws = serv.getPort(new QName(namespace,\r
// "ClustalWSPort"), Annotation.class);\r
\r
- Annotation<AAConWS> msaws = serv.getPort(new QName(namespace,\r
- "AAConWSPort"), Annotation.class);\r
-\r
// List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
// AAConTester.test_alignment_input));\r
\r
+ File.separator + "TO1381.fasta.aln"));\r
\r
try {\r
- System.out.println("Pres: "\r
- + msaws.getPresets().getPresets().get(0));\r
+ System.out.println("Pres: " + msaws.getPresets().getPresets());\r
String jobId = msaws.analize(fsl);\r
System.out.println("J: " + jobId);\r
HashSet<Score> result = msaws.getConservation(jobId);\r
assertNotNull(scores);\r
assertEquals(scores.size(), 568);\r
\r
+ // Using presets\r
+ PresetManager<AACon> presets = msaws.getPresets();\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Quick conservation"));\r
+ result = msaws.getConservation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.size(), 13);\r
+\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Slow conservation"));\r
+ result = msaws.getConservation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.size(), 5);\r
+\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Complete conservation"));\r
+ result = msaws.getConservation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.size(), 18);\r
+\r
+ } catch (UnsupportedRuntimeException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (LimitExceededException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (WrongParameterException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+\r
+ }\r
+\r
+ @Test\r
+ public void testPresetAnalize() throws FileNotFoundException, IOException {\r
+\r
+ String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
+ + File.separator;\r
+\r
+ List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
+ CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
+ + File.separator + "TO1381.fasta.aln"));\r
+\r
+ try {\r
+ System.out.println("Pres: " + msaws.getPresets().getPresets());\r
+\r
+ // Using presets\r
+ PresetManager<AACon> presets = msaws.getPresets();\r
+ String jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Quick conservation"));\r
+ HashSet<Score> result = msaws.getConservation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.size(), 13);\r
+\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Slow conservation"));\r
+ result = msaws.getConservation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.size(), 5);\r
+\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Complete conservation"));\r
+ result = msaws.getConservation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.size(), 18);\r
+\r
} catch (UnsupportedRuntimeException e) {\r
e.printStackTrace();\r
fail(e.getMessage());\r
} catch (ResultNotAvailableException e) {\r
e.printStackTrace();\r
fail(e.getMessage());\r
+ } catch (WrongParameterException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
}\r
\r
}\r
+\r
+ @Test\r
+ public void testCustomAnalize() throws FileNotFoundException, IOException {\r
+\r
+ String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
+ + File.separator;\r
+\r
+ List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
+ CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
+ + File.separator + "TO1381.fasta.aln"));\r
+\r
+ // Using options\r
+ RunnerConfig<AACon> options = msaws.getRunnerOptions();\r
+ // System.out.println(options.getArguments());\r
+\r
+ try {\r
+ options.getArgument("Calculation method").setDefaultValue("SMERFS");\r
+ String jobId = msaws.customAnalize(fsl, options.getArguments());\r
+ HashSet<Score> result = msaws.getConservation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.size(), 1);\r
+ assertEquals(\r
+ new ArrayList<Score>(result).get(0).getScores().get(0),\r
+ 0.698f);\r
+\r
+ options.getArgument("Calculation method").setDefaultValue("SMERFS");\r
+ options.removeArgument("Normalize");\r
+ System.out.println(options);\r
+ jobId = msaws.customAnalize(fsl, options.getArguments());\r
+ result = msaws.getConservation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.size(), 1);\r
+ assertEquals(\r
+ new ArrayList<Score>(result).get(0).getScores().get(0),\r
+ 0.401f);\r
+\r
+ } catch (WrongParameterException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (UnsupportedRuntimeException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (LimitExceededException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
}\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
-import compbio.data.sequence.FastaSequence;\r
\r
@XmlRootElement(name = "align", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class Align {\r
\r
@XmlElement(name = "fastaSequences", namespace = "")\r
- private List<FastaSequence> fastaSequences;\r
+ private List<compbio.data.sequence.FastaSequence> fastaSequences;\r
\r
/**\r
* \r
* @return\r
* returns List<FastaSequence>\r
*/\r
- public List<FastaSequence> getFastaSequences() {\r
+ public List<compbio.data.sequence.FastaSequence> getFastaSequences() {\r
return this.fastaSequences;\r
}\r
\r
* @param fastaSequences\r
* the value for the fastaSequences property\r
*/\r
- public void setFastaSequences(List<FastaSequence> fastaSequences) {\r
+ public void setFastaSequences(List<compbio.data.sequence.FastaSequence> fastaSequences) {\r
this.fastaSequences = fastaSequences;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
-import compbio.data.sequence.FastaSequence;\r
\r
@XmlRootElement(name = "analize", namespace = "http://msa.data.compbio/01/12/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class Analize {\r
\r
@XmlElement(name = "fastaSequences", namespace = "")\r
- private List<FastaSequence> fastaSequences;\r
+ private List<compbio.data.sequence.FastaSequence> fastaSequences;\r
\r
/**\r
* \r
* @return\r
* returns List<FastaSequence>\r
*/\r
- public List<FastaSequence> getFastaSequences() {\r
+ public List<compbio.data.sequence.FastaSequence> getFastaSequences() {\r
return this.fastaSequences;\r
}\r
\r
* @param fastaSequences\r
* the value for the fastaSequences property\r
*/\r
- public void setFastaSequences(List<FastaSequence> fastaSequences) {\r
+ public void setFastaSequences(List<compbio.data.sequence.FastaSequence> fastaSequences) {\r
this.fastaSequences = fastaSequences;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
-import compbio.data.sequence.FastaSequence;\r
-import compbio.metadata.Option;\r
\r
@XmlRootElement(name = "customAlign", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class CustomAlign {\r
\r
@XmlElement(name = "fastaSequences", namespace = "")\r
- private List<FastaSequence> fastaSequences;\r
+ private List<compbio.data.sequence.FastaSequence> fastaSequences;\r
@XmlElement(name = "options", namespace = "")\r
- private List<Option> options;\r
+ private List<compbio.metadata.Option> options;\r
\r
/**\r
* \r
* @return\r
* returns List<FastaSequence>\r
*/\r
- public List<FastaSequence> getFastaSequences() {\r
+ public List<compbio.data.sequence.FastaSequence> getFastaSequences() {\r
return this.fastaSequences;\r
}\r
\r
* @param fastaSequences\r
* the value for the fastaSequences property\r
*/\r
- public void setFastaSequences(List<FastaSequence> fastaSequences) {\r
+ public void setFastaSequences(List<compbio.data.sequence.FastaSequence> fastaSequences) {\r
this.fastaSequences = fastaSequences;\r
}\r
\r
* @return\r
* returns List<Option>\r
*/\r
- public List<Option> getOptions() {\r
+ public List<compbio.metadata.Option> getOptions() {\r
return this.options;\r
}\r
\r
* @param options\r
* the value for the options property\r
*/\r
- public void setOptions(List<Option> options) {\r
+ public void setOptions(List<compbio.metadata.Option> options) {\r
this.options = options;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
-import compbio.data.sequence.FastaSequence;\r
-import compbio.metadata.Option;\r
\r
@XmlRootElement(name = "customAnalize", namespace = "http://msa.data.compbio/01/12/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class CustomAnalize {\r
\r
@XmlElement(name = "fastaSequences", namespace = "")\r
- private List<FastaSequence> fastaSequences;\r
+ private List<compbio.data.sequence.FastaSequence> fastaSequences;\r
@XmlElement(name = "options", namespace = "")\r
- private List<Option> options;\r
+ private List<compbio.metadata.Option> options;\r
\r
/**\r
* \r
* @return\r
* returns List<FastaSequence>\r
*/\r
- public List<FastaSequence> getFastaSequences() {\r
+ public List<compbio.data.sequence.FastaSequence> getFastaSequences() {\r
return this.fastaSequences;\r
}\r
\r
* @param fastaSequences\r
* the value for the fastaSequences property\r
*/\r
- public void setFastaSequences(List<FastaSequence> fastaSequences) {\r
+ public void setFastaSequences(List<compbio.data.sequence.FastaSequence> fastaSequences) {\r
this.fastaSequences = fastaSequences;\r
}\r
\r
* @return\r
* returns List<Option>\r
*/\r
- public List<Option> getOptions() {\r
+ public List<compbio.metadata.Option> getOptions() {\r
return this.options;\r
}\r
\r
* @param options\r
* the value for the options property\r
*/\r
- public void setOptions(List<Option> options) {\r
+ public void setOptions(List<compbio.metadata.Option> options) {\r
this.options = options;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
-import compbio.metadata.JobStatus;\r
\r
@XmlRootElement(name = "getJobStatusResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class GetJobStatusResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private JobStatus _return;\r
+ private compbio.metadata.JobStatus _return;\r
\r
/**\r
* \r
* @return\r
* returns JobStatus\r
*/\r
- public JobStatus getReturn() {\r
+ public compbio.metadata.JobStatus getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(JobStatus _return) {\r
+ public void setReturn(compbio.metadata.JobStatus _return) {\r
this._return = _return;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
-import compbio.metadata.Limit;\r
\r
@XmlRootElement(name = "getLimitResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class GetLimitResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private Limit _return;\r
+ private compbio.metadata.Limit _return;\r
\r
/**\r
* \r
* @return\r
* returns Limit\r
*/\r
- public Limit getReturn() {\r
+ public compbio.metadata.Limit getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(Limit _return) {\r
+ public void setReturn(compbio.metadata.Limit _return) {\r
this._return = _return;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
-import compbio.metadata.LimitsManager;\r
\r
@XmlRootElement(name = "getLimitsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class GetLimitsResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private LimitsManager _return;\r
+ private compbio.metadata.LimitsManager _return;\r
\r
/**\r
* \r
* @return\r
* returns LimitsManager\r
*/\r
- public LimitsManager getReturn() {\r
+ public compbio.metadata.LimitsManager getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(LimitsManager _return) {\r
+ public void setReturn(compbio.metadata.LimitsManager _return) {\r
this._return = _return;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
-import compbio.metadata.PresetManager;\r
\r
@XmlRootElement(name = "getPresetsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class GetPresetsResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private PresetManager _return;\r
+ private compbio.metadata.PresetManager _return;\r
\r
/**\r
* \r
* @return\r
* returns PresetManager\r
*/\r
- public PresetManager getReturn() {\r
+ public compbio.metadata.PresetManager getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(PresetManager _return) {\r
+ public void setReturn(compbio.metadata.PresetManager _return) {\r
this._return = _return;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
-import compbio.data.sequence.Alignment;\r
\r
@XmlRootElement(name = "getResultResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class GetResultResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private Alignment _return;\r
+ private compbio.data.sequence.Alignment _return;\r
\r
/**\r
* \r
* @return\r
* returns Alignment\r
*/\r
- public Alignment getReturn() {\r
+ public compbio.data.sequence.Alignment getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(Alignment _return) {\r
+ public void setReturn(compbio.data.sequence.Alignment _return) {\r
this._return = _return;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
-import compbio.metadata.RunnerConfig;\r
\r
@XmlRootElement(name = "getRunnerOptionsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class GetRunnerOptionsResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private RunnerConfig _return;\r
+ private compbio.metadata.RunnerConfig _return;\r
\r
/**\r
* \r
* @return\r
* returns RunnerConfig\r
*/\r
- public RunnerConfig getReturn() {\r
+ public compbio.metadata.RunnerConfig getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(RunnerConfig _return) {\r
+ public void setReturn(compbio.metadata.RunnerConfig _return) {\r
this._return = _return;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
-import compbio.data.sequence.FastaSequence;\r
-import compbio.metadata.Preset;\r
\r
@XmlRootElement(name = "presetAlign", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class PresetAlign {\r
\r
@XmlElement(name = "fastaSequences", namespace = "")\r
- private List<FastaSequence> fastaSequences;\r
+ private List<compbio.data.sequence.FastaSequence> fastaSequences;\r
@XmlElement(name = "preset", namespace = "")\r
- private Preset preset;\r
+ private compbio.metadata.Preset preset;\r
\r
/**\r
* \r
* @return\r
* returns List<FastaSequence>\r
*/\r
- public List<FastaSequence> getFastaSequences() {\r
+ public List<compbio.data.sequence.FastaSequence> getFastaSequences() {\r
return this.fastaSequences;\r
}\r
\r
* @param fastaSequences\r
* the value for the fastaSequences property\r
*/\r
- public void setFastaSequences(List<FastaSequence> fastaSequences) {\r
+ public void setFastaSequences(List<compbio.data.sequence.FastaSequence> fastaSequences) {\r
this.fastaSequences = fastaSequences;\r
}\r
\r
* @return\r
* returns Preset\r
*/\r
- public Preset getPreset() {\r
+ public compbio.metadata.Preset getPreset() {\r
return this.preset;\r
}\r
\r
* @param preset\r
* the value for the preset property\r
*/\r
- public void setPreset(Preset preset) {\r
+ public void setPreset(compbio.metadata.Preset preset) {\r
this.preset = preset;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
-import compbio.data.sequence.FastaSequence;\r
-import compbio.metadata.Preset;\r
\r
@XmlRootElement(name = "presetAnalize", namespace = "http://msa.data.compbio/01/12/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class PresetAnalize {\r
\r
@XmlElement(name = "fastaSequences", namespace = "")\r
- private List<FastaSequence> fastaSequences;\r
+ private List<compbio.data.sequence.FastaSequence> fastaSequences;\r
@XmlElement(name = "preset", namespace = "")\r
- private Preset preset;\r
+ private compbio.metadata.Preset preset;\r
\r
/**\r
* \r
* @return\r
* returns List<FastaSequence>\r
*/\r
- public List<FastaSequence> getFastaSequences() {\r
+ public List<compbio.data.sequence.FastaSequence> getFastaSequences() {\r
return this.fastaSequences;\r
}\r
\r
* @param fastaSequences\r
* the value for the fastaSequences property\r
*/\r
- public void setFastaSequences(List<FastaSequence> fastaSequences) {\r
+ public void setFastaSequences(List<compbio.data.sequence.FastaSequence> fastaSequences) {\r
this.fastaSequences = fastaSequences;\r
}\r
\r
* @return\r
* returns Preset\r
*/\r
- public Preset getPreset() {\r
+ public compbio.metadata.Preset getPreset() {\r
return this.preset;\r
}\r
\r
* @param preset\r
* the value for the preset property\r
*/\r
- public void setPreset(Preset preset) {\r
+ public void setPreset(compbio.metadata.Preset preset) {\r
this.preset = preset;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
-import compbio.metadata.ChunkHolder;\r
\r
@XmlRootElement(name = "pullExecStatisticsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class PullExecStatisticsResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private ChunkHolder _return;\r
+ private compbio.metadata.ChunkHolder _return;\r
\r
/**\r
* \r
* @return\r
* returns ChunkHolder\r
*/\r
- public ChunkHolder getReturn() {\r
+ public compbio.metadata.ChunkHolder getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(ChunkHolder _return) {\r
+ public void setReturn(compbio.metadata.ChunkHolder _return) {\r
this._return = _return;\r
}\r
\r
import java.util.ArrayList;\r
import java.util.List;\r
\r
+import org.apache.log4j.Logger;\r
+\r
import compbio.data.sequence.FastaSequence;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
\r
public final class WSUtil {\r
\r
+ private static Logger log = Logger.getLogger(WSUtil.class);\r
+\r
public static final void validateJobId(String jobId)\r
throws InvalidParameterException {\r
if (!compbio.engine.client.Util.isValidJobId(jobId)) {\r
git://source.jalview.org / jabaws.git / commitdiff